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Python script to simultaneously generate multiple pdbqt files for AutoDockTools?

Bioinformatics Asked by sasam on August 18, 2021

I have a folder of pdb ligand structures that I’d like to test in some docking experiments with a certain protein using AutoDock Vina.
I am not familiar with Python so I’ve always been using the interactive procedure on AutoDockTools to prepare the pdbqt ligand files instead of the prepare_ligand4.py script.
Could you please help me understand how to iterate this python script in a way that it can be applied to a set of pdb ligand files in order to create the corresponding set of pdbqt ligand files?
Thank you!

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